William Nickols
| Snapshot Date: 2025-12-22 13:45 -0500 (Mon, 22 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-25 11:59 -0500 (Thu, 25 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2025-12-23 11:28:10 -0000 (Tue, 23 Dec 2025) |
| EndedAt: 2025-12-23 11:45:16 -0000 (Tue, 23 Dec 2025) |
| EllapsedTime: 1025.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 62.141 0.357 63.053
maaslin_plot_results_from_output 62.119 0.361 63.232
maaslin3 28.450 0.682 29.203
maaslin_contrast_test 28.728 0.399 29.213
maaslin_write_results_lefse_format 24.473 0.087 24.809
maaslin_write_results 23.550 0.278 24.072
maaslin_fit 20.392 0.122 20.568
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-12-23 11:36:48.054451 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:36:48.19324 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:36:48.353066 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:36:48.392836 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:36:48.450577 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:36:48.599004 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:36:48.608343 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:36:48.629485 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:36:48.808386 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:36:48.817903 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:36:48.911597 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:36:48.994565 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:36:49.01308 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:36:49.077863 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:36:49.188562 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:37:12.298578 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:37:12.440344 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:37:12.599187 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:37:12.636108 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:37:12.693672 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:37:12.820548 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:37:12.829233 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:37:12.848967 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:37:13.0086 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:37:13.017197 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:37:13.099099 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:37:13.179637 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:37:13.200252 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:37:13.273121 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:37:13.393588 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:37:46.149369 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:37:46.278169 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:37:46.407944 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:37:46.444915 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:37:46.502902 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:37:46.639141 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:37:46.648595 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:37:46.669991 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:37:46.836955 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:37:46.846136 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:37:46.93456 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:37:47.006265 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:37:47.026536 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:37:47.097106 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:37:47.219579 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:38:07.395027 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:38:07.525925 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:38:07.656838 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:38:07.694318 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:38:07.754479 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:38:07.88733 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:38:07.89615 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:38:07.916692 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:38:08.117647 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:38:08.127009 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:38:08.216461 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:38:08.294253 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:38:08.313699 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:38:08.378651 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:38:08.489342 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:38:08.780956 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/residuals_linear.rds
2025-12-23 11:38:08.84956 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/fitted_linear.rds
2025-12-23 11:38:08.920298 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/residuals_logistic.rds
2025-12-23 11:38:09.265814 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/fitted_logistic.rds
2025-12-23 11:38:38.442196 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:38:38.576187 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:38:38.710305 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:38:38.75082 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:38:38.811631 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:38:38.950992 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:38:38.960083 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:38:38.980695 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:38:39.171239 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:38:39.179703 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:38:39.258335 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:38:39.323433 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:38:39.343055 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:38:39.409295 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:38:39.524363 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:38:58.418976 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:38:58.5444 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:38:58.66629 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:38:58.701303 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:38:58.757222 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:38:58.88089 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:38:58.889104 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:38:58.90792 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:38:59.069811 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:38:59.078379 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:38:59.163762 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:38:59.233474 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:38:59.253817 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:38:59.322605 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:38:59.433537 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:38:59.751608 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/residuals_linear.rds
2025-12-23 11:38:59.819593 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/fitted_linear.rds
2025-12-23 11:38:59.889378 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/residuals_logistic.rds
2025-12-23 11:39:00.232509 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/fitted_logistic.rds
2025-12-23 11:39:28.50203 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:39:28.624782 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:39:28.74652 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:39:28.782128 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:39:28.838477 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:39:28.961656 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:39:28.970113 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:39:28.989001 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:39:29.181731 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:39:29.191004 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:39:29.277459 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:39:29.345621 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:39:29.365557 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:39:29.43356 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:39:29.561454 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:39:48.623281 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:39:48.783868 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:39:48.913487 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:39:48.949292 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:39:49.007 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:39:49.132364 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:39:49.141105 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:39:49.160799 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:39:49.315808 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:39:49.324382 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:39:49.406342 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:39:49.470786 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:39:49.490271 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:39:49.556917 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:39:49.671353 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:39:49.961147 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/residuals_linear.rds
2025-12-23 11:39:50.02932 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/fitted_linear.rds
2025-12-23 11:39:50.099992 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/residuals_logistic.rds
2025-12-23 11:39:50.44158 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d039213cd4/fits/fitted_logistic.rds
2025-12-23 11:40:18.319886 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:40:18.446913 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:40:18.571784 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:40:18.607674 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:40:18.6648 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:40:18.791447 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:40:18.799828 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:40:18.819583 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:40:18.989366 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:40:18.998365 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:40:19.087368 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:40:19.159846 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:40:19.181817 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:40:19.248412 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:40:19.364285 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:40:38.344179 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:40:38.472367 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:40:38.593816 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:40:38.629064 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:40:38.684873 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:40:38.807988 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:40:38.816734 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:40:38.836156 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:40:38.988839 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:40:38.997224 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:40:39.077595 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:40:39.143237 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:40:39.162812 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:40:39.228166 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:40:39.384444 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:41:11.861781 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:41:27.004591 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:42:01.016995 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:42:16.319998 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:42:17.250726 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_linear.rds
2025-12-23 11:42:17.320382 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_linear.rds
2025-12-23 11:42:17.364228 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_logistic.rds
2025-12-23 11:42:17.444416 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_logistic.rds
2025-12-23 11:42:48.187908 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:42:57.766366 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:42:58.273806 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_linear.rds
2025-12-23 11:42:58.33692 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_linear.rds
2025-12-23 11:42:58.37796 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_logistic.rds
2025-12-23 11:42:58.450793 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_logistic.rds
2025-12-23 11:43:24.448044 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:43:34.037329 WARNING::Fitting problem for feature 124 returning NA
2025-12-23 11:43:34.54097 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_linear.rds
2025-12-23 11:43:34.611038 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_linear.rds
2025-12-23 11:43:34.655468 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_logistic.rds
2025-12-23 11:43:34.736959 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_logistic.rds
2025-12-23 11:43:59.59698 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:43:59.733966 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:43:59.869277 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:43:59.909753 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:43:59.972934 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:44:00.115495 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:44:00.12519 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:44:00.147051 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:44:00.321435 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:44:00.33042 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:44:00.414329 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:44:00.482284 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:44:00.502277 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:44:00.568847 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:44:00.687085 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:44:20.888052 WARNING::Fitting problem for feature 50 returning NA
2025-12-23 11:44:21.031071 WARNING::Fitting problem for feature 62 returning NA
2025-12-23 11:44:21.171704 WARNING::Fitting problem for feature 74 returning NA
2025-12-23 11:44:21.215465 WARNING::Fitting problem for feature 78 returning NA
2025-12-23 11:44:21.282977 WARNING::Fitting problem for feature 84 returning NA
2025-12-23 11:44:21.420671 WARNING::Fitting problem for feature 96 returning NA
2025-12-23 11:44:21.43028 WARNING::Fitting problem for feature 97 returning NA
2025-12-23 11:44:21.450515 WARNING::Fitting problem for feature 99 returning NA
2025-12-23 11:44:21.620561 WARNING::Fitting problem for feature 114 returning NA
2025-12-23 11:44:21.629821 WARNING::Fitting problem for feature 115 returning NA
2025-12-23 11:44:21.718717 WARNING::Fitting problem for feature 123 returning NA
2025-12-23 11:44:21.790852 WARNING::Fitting problem for feature 130 returning NA
2025-12-23 11:44:21.811544 WARNING::Fitting problem for feature 132 returning NA
2025-12-23 11:44:21.887684 WARNING::Fitting problem for feature 139 returning NA
2025-12-23 11:44:22.013105 WARNING::Fitting problem for feature 150 returning NA
2025-12-23 11:44:22.438096 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_linear.rds
2025-12-23 11:44:22.507603 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_linear.rds
2025-12-23 11:44:22.578824 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/residuals_logistic.rds
2025-12-23 11:44:22.927541 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d063a7f8e6/fits/fitted_logistic.rds
2025-12-23 11:44:51.551599 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-23 11:44:51.578502 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-23 11:44:51.596939 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-23 11:44:51.680526 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-23 11:44:51.707233 ERROR::Effect name not found in metadata: d
2025-12-23 11:44:51.72543 ERROR::No user formula provided
2025-12-23 11:44:51.773348 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-23 11:44:51.791596 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-23 11:44:56.933336 INFO::Writing function arguments to log file
2025-12-23 11:44:56.95867 INFO::Verifying options selected are valid
2025-12-23 11:45:00.492168 INFO::Writing function arguments to log file
2025-12-23 11:45:00.515189 INFO::Verifying options selected are valid
2025-12-23 11:45:00.517092 INFO::Determining format of input files
2025-12-23 11:45:00.519112 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-23 11:45:00.523619 INFO::Running selected normalization method: TSS
2025-12-23 11:45:00.526248 INFO::Creating output feature tables folder
2025-12-23 11:45:00.528073 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/features/data_norm.tsv
2025-12-23 11:45:00.530848 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-23 11:45:00.532736 INFO::Total samples in data: 16
2025-12-23 11:45:00.53466 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-23 11:45:00.536384 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-23 11:45:00.540051 INFO::Total filtered features: 0
2025-12-23 11:45:00.542191 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-23 11:45:00.544399 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-23 11:45:00.546344 INFO::Filtered feature names from variance filtering:
2025-12-23 11:45:00.548146 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/features/filtered_data.tsv
2025-12-23 11:45:00.551102 INFO::Running selected transform method: LOG
2025-12-23 11:45:00.553452 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/features/data_transformed.tsv
2025-12-23 11:45:00.556844 INFO::Applying z-score to standardize continuous metadata
2025-12-23 11:45:00.566407 INFO::Running the linear model component
2025-12-23 11:45:00.594177 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:00.602532 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:00.611184 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:00.624558 INFO::Counting total values for each feature
2025-12-23 11:45:00.628222 INFO::Running the logistic model component
2025-12-23 11:45:00.657205 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:00.670288 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:00.683635 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:00.702496 INFO::Counting total values for each feature
2025-12-23 11:45:00.707215 INFO::Re-running abundances for warn_prevalence
2025-12-23 11:45:00.70952 INFO::Running selected normalization method: TSS
2025-12-23 11:45:00.712979 INFO::Running selected transform method: LOG
2025-12-23 11:45:00.739841 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:00.748613 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:00.757647 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:00.943045 INFO::Creating fits folder
2025-12-23 11:45:00.945085 INFO::Writing residuals to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/fits/residuals_linear.rds
2025-12-23 11:45:00.947167 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/fits/fitted_linear.rds
2025-12-23 11:45:00.949386 INFO::Writing residuals to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/fits/residuals_logistic.rds
2025-12-23 11:45:00.951644 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/fits/fitted_logistic.rds
2025-12-23 11:45:00.95651 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/all_results.tsv
2025-12-23 11:45:00.959781 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/significant_results.tsv
2025-12-23 11:45:00.962386 INFO::Creating output figures folder
2025-12-23 11:45:00.965009 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/figures/summary_plot.pdf
2025-12-23 11:45:03.445675 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/figures
2025-12-23 11:45:03.448498 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-23 11:45:03.456496 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-23 11:45:04.207649 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/figures/summary_plot.pdf
2025-12-23 11:45:06.71878 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmptWwXBf/file2e91d030969172/figures
2025-12-23 11:45:06.721148 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-23 11:45:06.728956 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-23 11:45:07.490883 INFO::Running the linear model component
2025-12-23 11:45:07.504981 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:07.511591 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:07.518332 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:07.529297 INFO::Counting total values for each feature
2025-12-23 11:45:07.531986 INFO::Running the logistic model component
2025-12-23 11:45:07.545177 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:07.554481 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:07.56351 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:07.576716 INFO::Counting total values for each feature
2025-12-23 11:45:07.579737 INFO::Re-running abundances for warn_prevalence
2025-12-23 11:45:07.580872 INFO::Running selected normalization method: TSS
2025-12-23 11:45:07.582824 INFO::Running selected transform method: LOG
2025-12-23 11:45:07.596072 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:07.602662 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:07.609076 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:07.740952 INFO::Creating output folder
2025-12-23 11:45:07.742389 INFO::Creating output figures folder
2025-12-23 11:45:07.744257 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmptWwXBf/file2e91d06f6d0f26/figures/summary_plot.pdf
2025-12-23 11:45:10.085127 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmptWwXBf/file2e91d06f6d0f26/figures
2025-12-23 11:45:10.087597 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-23 11:45:10.094999 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-23 11:45:11.465837 INFO::Applying z-score to standardize continuous metadata
2025-12-23 11:45:11.477657 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-23 11:45:11.478985 INFO::Bypass z-score application to metadata
2025-12-23 11:45:11.482985 INFO::Bypass z-score application to metadata
2025-12-23 11:45:11.510683 INFO::Determining format of input files
2025-12-23 11:45:11.512157 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-23 11:45:11.513639 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-23 11:45:11.525366 INFO::Determining format of input files
2025-12-23 11:45:11.527045 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-23 11:45:11.529126 INFO::Input format is feature_specific_covariate samples as columns
2025-12-23 11:45:11.541357 INFO::Determining format of input files
2025-12-23 11:45:11.54294 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-23 11:45:11.544502 INFO::Input format is feature_specific_covariate samples as columns
2025-12-23 11:45:11.547213 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-23 11:45:11.548509 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-23 11:45:11.565385 INFO::Running selected transform method: LOG
2025-12-23 11:45:11.567153 INFO::Creating output feature tables folder
2025-12-23 11:45:11.568591 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d07bfe9fc6/features/data_transformed.tsv
2025-12-23 11:45:11.574889 INFO::Running selected transform method: LOG
2025-12-23 11:45:11.57679 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d07bfe9fc6/features/data_transformed.tsv
2025-12-23 11:45:11.582984 INFO::Running selected transform method: PLOG
2025-12-23 11:45:11.585781 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d07bfe9fc6/features/data_transformed.tsv
2025-12-23 11:45:11.590589 INFO::Running selected transform method: NONE
2025-12-23 11:45:11.592058 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d07bfe9fc6/features/data_transformed.tsv
2025-12-23 11:45:11.603133 INFO::Running the linear model component
2025-12-23 11:45:11.617309 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:11.624448 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:11.631546 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:11.642849 INFO::Counting total values for each feature
2025-12-23 11:45:11.645626 INFO::Running the logistic model component
2025-12-23 11:45:11.659942 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:11.670556 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:11.680774 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:11.695598 INFO::Counting total values for each feature
2025-12-23 11:45:11.698932 INFO::Re-running abundances for warn_prevalence
2025-12-23 11:45:11.700311 INFO::Running selected normalization method: TSS
2025-12-23 11:45:11.702698 INFO::Running selected transform method: LOG
2025-12-23 11:45:11.717233 INFO::Fitting model to feature number 1, a
2025-12-23 11:45:11.724332 INFO::Fitting model to feature number 2, b
2025-12-23 11:45:11.731385 INFO::Fitting model to feature number 3, c
2025-12-23 11:45:11.873944 INFO::Creating output folder
2025-12-23 11:45:11.875412 INFO::Creating fits folder
2025-12-23 11:45:11.876759 INFO::Writing residuals to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d036462c46/fits/residuals_linear.rds
2025-12-23 11:45:11.878225 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d036462c46/fits/fitted_linear.rds
2025-12-23 11:45:11.879807 INFO::Writing residuals to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d036462c46/fits/residuals_logistic.rds
2025-12-23 11:45:11.881365 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmptWwXBf/file2e91d036462c46/fits/fitted_logistic.rds
2025-12-23 11:45:11.885082 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmptWwXBf/file2e91d036462c46/all_results.tsv
2025-12-23 11:45:11.88762 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /home/biocbuild/tmp/RtmptWwXBf/file2e91d036462c46/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
510.777 4.790 517.574
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 28.450 | 0.682 | 29.203 | |
| maaslin_check_arguments | 0.205 | 0.004 | 0.209 | |
| maaslin_check_formula | 0.207 | 0.000 | 0.207 | |
| maaslin_compute_formula | 0.248 | 0.008 | 0.259 | |
| maaslin_contrast_test | 28.728 | 0.399 | 29.213 | |
| maaslin_filter | 0.635 | 0.004 | 0.640 | |
| maaslin_fit | 20.392 | 0.122 | 20.568 | |
| maaslin_log_arguments | 0.175 | 0.016 | 0.193 | |
| maaslin_normalize | 0.350 | 0.019 | 0.370 | |
| maaslin_plot_results | 62.141 | 0.357 | 63.053 | |
| maaslin_plot_results_from_output | 62.119 | 0.361 | 63.232 | |
| maaslin_process_metadata | 0.653 | 0.016 | 0.676 | |
| maaslin_read_data | 0.193 | 0.015 | 0.210 | |
| maaslin_reorder_data | 0.209 | 0.012 | 0.223 | |
| maaslin_transform | 0.826 | 0.031 | 0.866 | |
| maaslin_write_results | 23.550 | 0.278 | 24.072 | |
| maaslin_write_results_lefse_format | 24.473 | 0.087 | 24.809 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.006 | 0.000 | 0.007 | |